1-182576254-AC-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS2_Supporting
The NM_021133.4(RNASEL):c.2039+1delG variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.0000789 in 1,610,296 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021133.4 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 249362Hom.: 0 AF XY: 0.000149 AC XY: 20AN XY: 134598
GnomAD4 exome AF: 0.0000775 AC: 113AN: 1457978Hom.: 0 Cov.: 30 AF XY: 0.0000924 AC XY: 67AN XY: 724838
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74490
ClinVar
Submissions by phenotype
Prostate cancer, hereditary, 1 Uncertain:1
The splice donor variant c.2039+1del) in RNASEL gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The variant has 0.01% allele frequency in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. LOF in this gene have not been reported previously. For these reasons, this variant has been classified as Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at